Yea, some of that information is documented on the bootloader page (http://www.arduino.cc/en/Hacking/Bootloader), but it could certainly use some clarification and expansion. It wouldn't hurt to add it to the spec as well. I'm not sure that the reference needs to talk about the bootloader baud rate, but we definitely need better documentation of what serial communication is, how one can use it (e.g. how to talk over USB, via TTL serial, or over RS232), and what gets transmitted (e.g. binary vs. ASCII data). It's a top priority on the bugs list. Paul, if you wanted to write a tutorial on serial communication in general, that would be awesome.